Oh great... Another one. Hmmm I think this relates to the Battle of the Coral Sea...

Hmm, somehow... The Battle of the Coral Sea gave some major blow for the both carriers, Shoukaku was damaged by bombers while Zuikaku aircraft complement depletes.

The battle somehow makes the two carriers incapacitate for the carrier-massacre, Battle of Midway.

Also, USS Cavalla (AGSS-244) is the submarine that torpedoed Shoukaku during the Battle of Marianas (Great Turkey Shoot).

And the discrepancy between their Luck status.
Shoukaku kept getting the more terrible damage while Zuikaku survived. She's shielding her sister